Changeset 6469

Timestamp:

Nov 4, 2021, 11:26:45 AM (15 months ago)

Author:

Nicklas Nordborg

Message:

References #1347: Updates to registration of specimen handled by external lab

Changing the soft warning limits for the number of reads and improving the display by adding thousand separators.

Location:

extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/plugins/cmd

Files:

• DemuxInfo.java (modified) (1 diff)
• IntValidator.java (modified) (4 diffs)
• LongValidator.java (modified) (5 diffs)

extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/plugins/cmd/DemuxInfo.java

@@ -39 +39 @@
       software = demuxSection.getRequiredEntry("Software", SoftwareValidator.INSTANCE);
       readString = demuxSection.getRequiredEntry("ReadString", PatternValidator.READ_STRING);
-      pfReads = mergeSection.getRequiredEntry("PF_READS", LongValidator.POSITIVE.warnIf(10000000l, null)); // Warn if less than 10M reads
+      pfReads = mergeSection.getRequiredEntry("PF_READS", LongValidator.POSITIVE.warnIf(20000000l, 50000000l)); // Warn if less than 20M or more than 50M reads
       reads = pfReads; // 
       valid = !demuxSection.hasError() && !mergeSection.hasError();

extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/plugins/cmd/IntValidator.java

@@ -104 +104 @@
       catch (Exception ex)
       {
-        section.addErrorMessage("Invalid integer in JSON: "+entryKey+"="+value);
+        section.addErrorMessage("Invalid "+entryKey+" in JSON: "+value);
       }
     }
@@ -111 +111 @@
       if (minValue != null && result < minValue)
       {
-        section.addErrorMessage("Invalid integer in JSON: "+entryKey+"="+value+" (expected >="+minValue+")");
+        section.addErrorMessage("Invalid "+entryKey+" in JSON: "+value+" (expected >="+minValue+")");
         result = null;
       }
       if (maxValue != null && result > maxValue)
       {
-        section.addErrorMessage("Invalid integer in JSON: "+entryKey+"="+value+" (expected <="+maxValue+")");
+        section.addErrorMessage("Invalid "+entryKey+" in JSON: "+value+" (expected <="+maxValue+")");
         result = null;
       }
@@ -123 +123 @@
         if (allowed.indexOf(result) == -1)
         {
-          section.addErrorMessage("Invalid integer in JSON: "+entryKey+"="+value+" (expected one of "+allowed+")");
+          section.addErrorMessage("Invalid "+entryKey+" in JSON: "+value+" (expected one of "+allowed+")");
           result = null;
         }
@@ -132 +132 @@
       if (softMin != null && result < softMin)
       {
-        section.addWarningMessage("Unexpected integer in JSON: "+entryKey+"="+value+" (expected >="+softMin+")");
+        section.addWarningMessage("Low value for "+entryKey+" in JSON: "+value+" (expected >="+softMin+")");
       }
       if (softMax != null && result > softMax)
       {
-        section.addWarningMessage("Unexpected integer in JSON: "+entryKey+"="+value+" (expected <="+softMax+")");
+        section.addWarningMessage("High value for "+entryKey+" in JSON: "+value+" (expected <="+softMax+")");
       }
     }

extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/plugins/cmd/LongValidator.java

@@ -2 +2 @@
 
 import java.util.List;
+import java.util.Locale;
 
 import net.sf.basedb.core.DbControl;
@@ -119 +120 @@
       catch (Exception ex)
       {
-        section.addErrorMessage("Invalid long in JSON: "+entryKey+"="+value);
+        section.addErrorMessage("Invalid "+entryKey+" in JSON: "+value);
       }
     }
@@ -126 +127 @@
       if (minValue != null && result < minValue)
       {
-        section.addErrorMessage("Invalid long in JSON: "+entryKey+"="+value+" (expected >="+minValue+")");
+        section.addErrorMessage("Invalid "+entryKey+" in JSON: "+String.format(Locale.US, "%,d", value)+" (expected >="+String.format(Locale.US, "%,d", minValue)+")");
         result = null;
       }
       if (maxValue != null && result > maxValue)
       {
-        section.addErrorMessage("Invalid long in JSON: "+entryKey+"="+value+" (expected <="+maxValue+")");
+        section.addErrorMessage("Invalid "+entryKey+" in JSON: "+String.format(Locale.US, "%,d", value)+" (expected <="+String.format(Locale.US, "%,d", maxValue)+")");
         result = null;
       }
@@ -138 +139 @@
         if (allowed.indexOf(result) == -1)
         {
-          section.addErrorMessage("Invalid long in JSON: "+entryKey+"="+value+" (expected one of "+allowed+")");
+          section.addErrorMessage("Invalid "+entryKey+" in JSON: "+value+" (expected one of "+allowed+")");
           result = null;
         }
@@ -147 +148 @@
       if (softMin != null && result < softMin)
       {
-        section.addWarningMessage("Unexpected long in JSON: "+entryKey+"="+value+" (expected >="+softMin+")");
+        section.addWarningMessage("Low value for "+entryKey+" in JSON: "+String.format(Locale.US, "%,d", value)+" (expected >="+String.format(Locale.US, "%,d", softMin)+")");
       }
       if (softMax != null && result > softMax)
       {
-        section.addWarningMessage("Unexpected long in JSON: "+entryKey+"="+value+" (expected <="+softMax+")");
+        section.addWarningMessage("High value for "+entryKey+" in JSON: "+String.format(Locale.US, "%,d", value)+" (expected <="+String.format(Locale.US, "%,d", softMax)+")");
       }
     }